TRF5_YEAST
ID TRF5_YEAST Reviewed; 642 AA.
AC P48561; D6W0P5;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 29-MAY-2007, sequence version 2.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=Poly(A) RNA polymerase protein 1;
DE EC=2.7.7.19 {ECO:0000250|UniProtKB:P53632};
DE AltName: Full=Topoisomerase 1-related protein TRF5;
GN Name=TRF5; OrderedLocusNames=YNL299W; ORFNames=N0440;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RX PubMed=8710513; DOI=10.1093/nar/24.12.2404;
RA Castano I.B., Heath-Pagliuso S., Sadoff B.U., Fitzhugh D.J.,
RA Christman M.F.;
RT "A novel family of TRF (DNA topoisomerase I-related function) genes
RT required for proper nuclear segregation.";
RL Nucleic Acids Res. 24:2404-2410(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=8553702; DOI=10.1002/yea.320111311;
RA Maurer K.C.T., Urbanus J.H.M., Planta R.J.;
RT "Sequence analysis of a 30 kb DNA segment from yeast chromosome XIV
RT carrying a ribosomal protein gene cluster, the genes encoding a plasma
RT membrane protein and a subunit of replication factor C, and a novel
RT putative serine/threonine protein kinase gene.";
RL Yeast 11:1303-1310(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(1997).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [5]
RP FUNCTION.
RX PubMed=10926539; DOI=10.1126/science.289.5480.774;
RA Wang Z., Castano I.B., De Las Penas A., Adams C., Christman M.F.;
RT "Pol kappa: a DNA polymerase required for sister chromatid cohesion.";
RL Science 289:774-779(2000).
RN [6]
RP NOMENCLATURE.
RX PubMed=11579108; DOI=10.1074/jbc.r100056200;
RA Burgers P.M.J., Koonin E.V., Bruford E., Blanco L., Burtis K.C.,
RA Christman M.F., Copeland W.C., Friedberg E.C., Hanaoka F., Hinkle D.C.,
RA Lawrence C.W., Nakanishi M., Ohmori H., Prakash L., Prakash S.,
RA Reynaud C.-A., Sugino A., Todo T., Wang Z., Weill J.-C., Woodgate R.;
RT "Eukaryotic DNA polymerases: proposal for a revised nomenclature.";
RL J. Biol. Chem. 276:43487-43490(2001).
RN [7]
RP FUNCTION, AND INTERACTION WITH POL2; DPB2 AND DPB11.
RX PubMed=12665575; DOI=10.1128/mcb.23.8.2733-2748.2003;
RA Edwards S., Li C.M., Levy D.L., Brown J., Snow P.M., Campbell J.L.;
RT "Saccharomyces cerevisiae DNA polymerase epsilon and polymerase sigma
RT interact physically and functionally, suggesting a role for polymerase
RT epsilon in sister chromatid cohesion.";
RL Mol. Cell. Biol. 23:2733-2748(2003).
RN [8]
RP IDENTIFICATION OF FRAMESHIFT.
RX PubMed=12748633; DOI=10.1038/nature01644;
RA Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.;
RT "Sequencing and comparison of yeast species to identify genes and
RT regulatory elements.";
RL Nature 423:241-254(2003).
RN [9]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [10]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [11]
RP FUNCTION.
RX PubMed=16260630; DOI=10.1128/mcb.25.22.10183-10189.2005;
RA Haracska L., Johnson R.E., Prakash L., Prakash S.;
RT "Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit poly(A) RNA
RT polymerase activity but no DNA polymerase activity.";
RL Mol. Cell. Biol. 25:10183-10189(2005).
RN [12]
RP IDENTIFICATION IN THE TRAMP5 COMPLEX, AND FUNCTION OF THE TRAMP5 COMPLEX.
RX PubMed=16374505; DOI=10.1038/sj.embor.7400612;
RA Houseley J., Tollervey D.;
RT "Yeast Trf5p is a nuclear poly(A) polymerase.";
RL EMBO Rep. 7:205-211(2006).
RN [13]
RP FUNCTION.
RX PubMed=16373491; DOI=10.1261/rna.2207206;
RA Egecioglu D.E., Henras A.K., Chanfreau G.F.;
RT "Contributions of Trf4p- and Trf5p-dependent polyadenylation to the
RT processing and degradative functions of the yeast nuclear exosome.";
RL RNA 12:26-32(2006).
RN [14]
RP FUNCTION.
RX PubMed=16431988; DOI=10.1261/rna.2305406;
RA Kadaba S., Wang X., Anderson J.T.;
RT "Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent
RT polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S
RT rRNA.";
RL RNA 12:508-521(2006).
RN [15]
RP FUNCTION.
RX PubMed=17179095; DOI=10.1534/genetics.106.065987;
RA Reis C.C., Campbell J.L.;
RT "Contribution of Trf4/5 and the nuclear exosome to genome stability through
RT regulation of histone mRNA levels in Saccharomyces cerevisiae.";
RL Genetics 175:993-1010(2007).
RN [16]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-596 AND SER-602, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: Catalytic subunit of the TRAMP5 complex which has a poly(A)
CC RNA polymerase activity and is involved in a post-transcriptional
CC quality control mechanism limiting inappropriate expression of genetic
CC information. Polyadenylation is required for the degradative activity
CC of the exosome on several of its nuclear RNA substrates like cryptic
CC transcripts generated by RNA polymerase II and III, or hypomethylated
CC pre-tRNAi-Met. Polyadenylates RNA processing and degradation
CC intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains
CC lacking a functional exosome. TRF5 is also required for proper nuclear
CC division in mitosis and sister chromatid cohesion. Involved in the
CC regulation of histone mRNA levels. May mediate mitotic chromosome
CC condensation. {ECO:0000269|PubMed:10926539,
CC ECO:0000269|PubMed:12665575, ECO:0000269|PubMed:16260630,
CC ECO:0000269|PubMed:16373491, ECO:0000269|PubMed:16374505,
CC ECO:0000269|PubMed:16431988, ECO:0000269|PubMed:17179095,
CC ECO:0000269|PubMed:8710513}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide;
CC Xref=Rhea:RHEA:11332, Rhea:RHEA-COMP:14527, Rhea:RHEA-COMP:17347,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:140395,
CC ChEBI:CHEBI:173115; EC=2.7.7.19;
CC Evidence={ECO:0000250|UniProtKB:P53632};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC -!- SUBUNIT: Component of the TRAMP5 complex composed of at least AIR1,
CC MTR4 and TFR5. Interacts with POL2, DPB2 and DPB11.
CC {ECO:0000269|PubMed:12665575, ECO:0000269|PubMed:16374505}.
CC -!- INTERACTION:
CC P48561; P47047: MTR4; NbExp=6; IntAct=EBI-19525, EBI-11592;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 2240 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B-like family.
CC {ECO:0000305}.
CC -!- CAUTION: Was originally thought to have DNA polymerase activity.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC49099.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=AAC49397.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAA96217.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U47282; AAC49397.1; ALT_FRAME; Genomic_DNA.
DR EMBL; U23084; AAC49099.1; ALT_FRAME; Genomic_DNA.
DR EMBL; Z71575; CAA96217.1; ALT_FRAME; Genomic_DNA.
DR EMBL; BK006947; DAA10261.1; -; Genomic_DNA.
DR PIR; S60401; S60401.
DR RefSeq; NP_014100.2; NM_001183137.1.
DR AlphaFoldDB; P48561; -.
DR SMR; P48561; -.
DR BioGRID; 35539; 225.
DR ComplexPortal; CPX-1680; TRAMP complex variant 5-1.
DR ELM; P48561; -.
DR IntAct; P48561; 3.
DR MINT; P48561; -.
DR STRING; 4932.YNL299W; -.
DR iPTMnet; P48561; -.
DR MaxQB; P48561; -.
DR PaxDb; P48561; -.
DR PRIDE; P48561; -.
DR EnsemblFungi; YNL299W_mRNA; YNL299W; YNL299W.
DR GeneID; 855417; -.
DR KEGG; sce:YNL299W; -.
DR SGD; S000005243; TRF5.
DR VEuPathDB; FungiDB:YNL299W; -.
DR eggNOG; KOG1906; Eukaryota.
DR GeneTree; ENSGT00940000169468; -.
DR HOGENOM; CLU_013572_5_0_1; -.
DR InParanoid; P48561; -.
DR OMA; KMVHKAS; -.
DR BioCyc; YEAST:G3O-33287-MON; -.
DR BRENDA; 2.7.7.19; 984.
DR PRO; PR:P48561; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P48561; protein.
DR GO; GO:0005730; C:nucleolus; HDA:SGD.
DR GO; GO:0031499; C:TRAMP complex; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004652; F:polynucleotide adenylyltransferase activity; IDA:SGD.
DR GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0071044; P:histone mRNA catabolic process; IGI:SGD.
DR GO; GO:0043629; P:ncRNA polyadenylation; IGI:SGD.
DR GO; GO:0071039; P:nuclear polyadenylation-dependent CUT catabolic process; IGI:SGD.
DR GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IGI:SGD.
DR GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
DR GO; GO:0071036; P:nuclear polyadenylation-dependent snoRNA catabolic process; IGI:SGD.
DR GO; GO:0071037; P:nuclear polyadenylation-dependent snRNA catabolic process; IGI:SGD.
DR GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IGI:SGD.
DR GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IGI:SGD.
DR GO; GO:0031123; P:RNA 3'-end processing; IBA:GO_Central.
DR GO; GO:0000292; P:RNA fragment catabolic process; IC:ComplexPortal.
DR GO; GO:0071050; P:sno(s)RNA polyadenylation; IGI:SGD.
DR GO; GO:0034475; P:U4 snRNA 3'-end processing; IMP:SGD.
DR Gene3D; 3.30.460.10; -; 1.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR002058; PAP_assoc.
DR InterPro; IPR002934; Polymerase_NTP_transf_dom.
DR InterPro; IPR045862; Trf4-like.
DR PANTHER; PTHR23092; PTHR23092; 1.
DR Pfam; PF01909; NTP_transf_2; 1.
DR Pfam; PF03828; PAP_assoc; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
PE 1: Evidence at protein level;
KW Cell cycle; Cell division; Magnesium; Manganese; Metal-binding; Mitosis;
KW Nucleotidyltransferase; Nucleus; Phosphoprotein; Reference proteome;
KW Transferase.
FT CHAIN 1..642
FT /note="Poly(A) RNA polymerase protein 1"
FT /id="PRO_0000120316"
FT DOMAIN 368..428
FT /note="PAP-associated"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 84..104
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 535..642
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 84..100
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 535..552
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 579..595
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 600..631
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 233
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 235
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT MOD_RES 596
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 602
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT CONFLICT 354..355
FT /note="MH -> ID (in Ref. 1; AAC49397)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 642 AA; 74179 MW; 67D4CD75AEBAE1A4 CRC64;
MTRLKAKYSP TKGKRKEDKH TKRMRKSSFT RTQKMLEVFN DNRSHFNKYE SLAIDVEDDD
TFGNLVLMEN DKSDVDIPVI EEVTSSEDEQ RAESSKRNNS LEDNQDFIAF SDSSEDETEQ
IKEDDDERSS FLLTDEHEVS KLTSQQSLNT ESACNVEYPW IRNHCHSKQR RIADWLTSEI
KDFVHYISPS KNEIKCRNRT IDKLRRAVKE LWSDADLHVF GSFATDLYLP GSDIDCVVNS
RNRDKEDRNY IYELARHLKN KGLAIRMEVI VKTRVPIIKF IEPQSQLHID VSFERTNGLE
AAKLIREWLR DSPGLRELVL IIKQFLHSRR LNNVHTGGLG GFTVICLVYS FLNMHPRIKS
NDIDVLDNLG VLLIDFFELY GKNFGYDDVA ISISDGYASY IPKSCWRTLE PSRSKFSLAI
QDPGDPNNNI SRGSFNMKDI KKAFAGAFEL LVNKCWELNS ATFKDRVGKS ILGNVIKYRG
QKRDFNDERD LVQNKAIIEN ERYHKRRTRI VQEDLFINDT EDLPVEEIYK LDEPAKKKQK
AKKDKREGEI KKSAIPSPPP DFGVSRSKLK RKVKKTDQGS LLHQNNLSID DLMGLSENDQ
ESDQDQKGRD TPSGQDEKSP LETKTVDAQT RRDYWLSKGQ AL
